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Volumn 32, Issue 13, 2016, Pages 1966-1973

MetaKTSP: A meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BREAST TUMOR; DNA METHYLATION; FIBROSING ALVEOLITIS; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN; META ANALYSIS (TOPIC); METHODOLOGY; PROCEDURES; PROGNOSIS; SUPERVISED MACHINE LEARNING; VALIDATION STUDY;

EID: 85007227258     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw115     Document Type: Article
Times cited : (34)

References (53)
  • 1
    • 84908296177 scopus 로고    scopus 로고
    • Rank discriminants for predicting phenotypes from RNA expression
    • Afsari,B. et al. (2014) Rank discriminants for predicting phenotypes from RNA expression. Ann. Appl. Stat., 8, 1469-1491.
    • (2014) Ann. Appl. Stat. , vol.8 , pp. 1469-1491
    • Afsari, B.1
  • 2
    • 0347090327 scopus 로고    scopus 로고
    • Adjustment of systematic microarray data biases
    • Benito,M. et al. (2004) Adjustment of systematic microarray data biases. Bioinformatics, 20, i105-i114.
    • (2004) Bioinformatics , vol.20 , pp. i105-i114
    • Benito, M.1
  • 3
    • 84902519819 scopus 로고    scopus 로고
    • Cross-study validation for the assessment of prediction algorithms
    • Bernau,C. et al. (2014) Cross-study validation for the assessment of prediction algorithms. Bioinformatics, 30, i105-i112.
    • (2014) Bioinformatics , vol.30 , pp. i105-i112
    • Bernau, C.1
  • 4
    • 67649197934 scopus 로고    scopus 로고
    • Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction
    • Cheng,C. et al. (2009) Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction. Bioinformatics, 25, 1655-1661.
    • (2009) Bioinformatics , vol.25 , pp. 1655-1661
    • Cheng, C.1
  • 5
    • 68349126950 scopus 로고    scopus 로고
    • Microarray-based gene expression profiling as a clinical tool for breast cancer management: Are we there yet?
    • Correa,G. and Reis-Filho,J. (2009) Microarray-based gene expression profiling as a clinical tool for breast cancer management: are we there yet? Int. J. Surg. Pathol., 17, 285-302.
    • (2009) Int. J. Surg. Pathol. , vol.17 , pp. 285-302
    • Correa, G.1    Reis-Filho, J.2
  • 6
    • 80054061796 scopus 로고    scopus 로고
    • Hormone receptor and ERBB2 status in gene expression profiles of human breast tumor samples
    • Dvorkin-Gheva,A. and Hassell,J. (2011) Hormone receptor and ERBB2 status in gene expression profiles of human breast tumor samples. Plos One, 6, e26023.
    • (2011) Plos One , vol.6 , pp. e26023
    • Dvorkin-Gheva, A.1    Hassell, J.2
  • 8
    • 0002294353 scopus 로고
    • Questions and answers #14
    • Fisher,R. (1948) Questions and answers #14. Am. Stat., 2, 30-31.
    • (1948) Am. Stat. , vol.2 , pp. 30-31
    • Fisher, R.1
  • 9
    • 41149104381 scopus 로고    scopus 로고
    • Cross-study validation and combined analysis of gene expression microarray data
    • Garrett-Mayer,E. et al. (2008) Cross-study validation and combined analysis of gene expression microarray data. Biostatistics, 9, 333-354.
    • (2008) Biostatistics , vol.9 , pp. 333-354
    • Garrett-Mayer, E.1
  • 10
    • 18544368641 scopus 로고    scopus 로고
    • Expression Profiles from Pairwise mRNA Comparisons
    • Geman,D. et al. (2004) Expression Profiles from Pairwise mRNA Comparisons. Stat. Appl. Genet. Mol. Biol., 3, article 19.
    • (2004) Stat. Appl. Genet. Mol. Biol. , vol.3
    • Geman, D.1
  • 11
    • 84870341638 scopus 로고    scopus 로고
    • Why your new cancer biomarker may never work: Recurrent patterns and remarkable diversity in biomarker failures
    • Kern,S. (2012) Why your new cancer biomarker may never work: recurrent patterns and remarkable diversity in biomarker failures. Cancer Res., 72, 6097-6101.
    • (2012) Cancer Res. , vol.72 , pp. 6097-6101
    • Kern, S.1
  • 12
    • 84855897445 scopus 로고    scopus 로고
    • MetaQC: Objective quality control and inclusion/exclusion criteria for genomic meta-analysis
    • Kang,D. et al. (2012) MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. Nucleic Acids Res., 40, e15.
    • (2012) Nucleic Acids Res. , vol.40 , pp. e15
    • Kang, D.1
  • 13
    • 33746108159 scopus 로고    scopus 로고
    • A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
    • Kuo,W. et al. (2006) A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nat. Biotechnol., 24, 832-840.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 832-840
    • Kuo, W.1
  • 14
    • 84908140306 scopus 로고    scopus 로고
    • Measuring the effect of inter-study variability on estimating prediction error
    • Ma,S. et al. (2014) Measuring the effect of inter-study variability on estimating prediction error. PLoS One, 9, e110840.
    • (2014) PLoS One , vol.9 , pp. e110840
    • Ma, S.1
  • 15
    • 2942578063 scopus 로고    scopus 로고
    • A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen
    • Ma,X. et al. (2004) A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell, 5, 607-616.
    • (2004) Cancer Cell , vol.5 , pp. 607-616
    • Ma, X.1
  • 16
    • 84877806149 scopus 로고    scopus 로고
    • A simple and reproducible breast cancer prognostic test
    • Marchionni,L. et al. (2013) A simple and reproducible breast cancer prognostic test. BMC Genomics, 17, 336.
    • (2013) BMC Genomics , vol.17 , pp. 336
    • Marchionni, L.1
  • 17
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
    • MAQC Consortium et al. (2006) The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24, 1151-1161.
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1151-1161
    • Consortium, M.1
  • 18
    • 84886892985 scopus 로고    scopus 로고
    • Development of omics-based clinical tests for prognosis and therapy selection: The challenge of achieving statistical robustness and clinical utility
    • McShane,L. and Polley,M. Development of omics-based clinical tests for prognosis and therapy selection: The challenge of achieving statistical robustness and clinical utility. Clin. Trials, 10, 653-665.
    • Clin. Trials , vol.10 , pp. 653-665
    • McShane, L.1    Polley, M.2
  • 19
    • 77957786147 scopus 로고    scopus 로고
    • Module-based prediction approach for robust inter-study predictions in microarray data
    • Mi,Z. et al. (2010) Module-based prediction approach for robust inter-study predictions in microarray data. Bioinformatics, 26, 2586-2593.
    • (2010) Bioinformatics , vol.26 , pp. 2586-2593
    • Mi, Z.1
  • 20
    • 9144254108 scopus 로고    scopus 로고
    • Inter-platform comparability of microarrays in acute lymphoblastic leukemia
    • Mitchell,S. et al. (2004) Inter-platform comparability of microarrays in acute lymphoblastic leukemia. BMC Genomics, 5, 71.
    • (2004) BMC Genomics , vol.5 , pp. 71
    • Mitchell, S.1
  • 21
    • 79953062931 scopus 로고    scopus 로고
    • Genome-wide methylation analysis identifies epigenetically inactivated candidate tumour suppressor genes in renal cell carcinoma
    • Morris,M. et al. (2011) Genome-wide methylation analysis identifies epigenetically inactivated candidate tumour suppressor genes in renal cell carcinoma. Oncogene, 30, 1390-1401.
    • (2011) Oncogene , vol.30 , pp. 1390-1401
    • Morris, M.1
  • 22
    • 0000551189 scopus 로고    scopus 로고
    • Popular ensemble methods: An empirical study
    • Opitz,D. and Maclin,R. (1999) Popular ensemble methods: an empirical study. J. Artif. Intell. Res., 11, 169-198.
    • (1999) J. Artif. Intell. Res. , vol.11 , pp. 169-198
    • Opitz, D.1    Maclin, R.2
  • 23
    • 73949084229 scopus 로고    scopus 로고
    • Karl Pearson's meta-analysis revisited
    • Owen,A.B. (2009) Karl Pearson's meta-analysis revisited. Ann. Stat., 37, 3867-3892.
    • (2009) Ann. Stat. , vol.37 , pp. 3867-3892
    • Owen, A.B.1
  • 24
    • 19944422061 scopus 로고    scopus 로고
    • A multigene assay to predict recurrence of tamoxifentreated, node-negative breast cancer
    • Paik,S. et al. (2004) A multigene assay to predict recurrence of tamoxifentreated, node-negative breast cancer. N. Engl. J. Med., 351, 2817-2826.
    • (2004) N. Engl. J. Med. , vol.351 , pp. 2817-2826
    • Paik, S.1
  • 25
    • 62449131093 scopus 로고    scopus 로고
    • Supervised risk predictor of breast cancer based on intrinsic subtypes
    • Parker,J. et al. (2009) Supervised risk predictor of breast cancer based on intrinsic subtypes. J. Clin. Oncol., 27, 1160-1167.
    • (2009) J. Clin. Oncol. , vol.27 , pp. 1160-1167
    • Parker, J.1
  • 26
    • 77955101694 scopus 로고    scopus 로고
    • Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma
    • Parris,T. et al. (2010) Clinical implications of gene dosage and gene expression patterns in diploid breast carcinoma. Clin. Cancer Res., 16, 3860-3874.
    • (2010) Clin. Cancer Res. , vol.16 , pp. 3860-3874
    • Parris, T.1
  • 27
    • 84894251319 scopus 로고    scopus 로고
    • DACH1: Its role as a classifier of long term good prognosis in luminal breast cancer
    • Powe, D. et al. (2014) DACH1: its role as a classifier of long term good prognosis in luminal breast cancer. PLoS One, 9, e84428.
    • (2014) PLoS One , vol.9 , pp. e84428
    • Powe, D.1
  • 28
    • 33847665105 scopus 로고    scopus 로고
    • Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas
    • Price,N. et al. (2007) Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas. Proc. Natl. Acad. Sci. USA, 104, 3414-3419.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 3414-3419
    • Price, N.1
  • 29
    • 0347201147 scopus 로고    scopus 로고
    • Multiclass cancer diagnosis using tumor gene expression signatures
    • Ramaswamy, S. et al. (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl. Acad. Sci. USA, 15149-15154.
    • (2001) Proc. Natl. Acad. Sci. USA , pp. 15149-15154
    • Ramaswamy, S.1
  • 30
    • 41949125894 scopus 로고    scopus 로고
    • A 2-gene classifier for predicting response to the farnesyltransferase inhibitor tipifarnib in acutemyeloid leukemia
    • Raponi,M. et al. (2008) A 2-gene classifier for predicting response to the farnesyltransferase inhibitor tipifarnib in acutemyeloid leukemia. Blood, 5, 2589-2596.
    • (2008) Blood , vol.5 , pp. 2589-2596
    • Raponi, M.1
  • 31
    • 77952821751 scopus 로고    scopus 로고
    • FOXC1 is a potential prognostic biomarker with functional significance in basal-like breast cancer
    • Ray,P. et al. (2010) FOXC1 is a potential prognostic biomarker with functional significance in basal-like breast cancer. Cancer Res., 70, 3870-3876.
    • (2010) Cancer Res. , vol.70 , pp. 3870-3876
    • Ray, P.1
  • 32
    • 21444453976 scopus 로고    scopus 로고
    • Limits of predictive models using microarray data for breast cancer clinical treatment outcome
    • Reid,J. et al. (2005) Limits of predictive models using microarray data for breast cancer clinical treatment outcome. J. Natl. Cancer Inst., 97, 927-930.
    • (2005) J. Natl. Cancer Inst. , vol.97 , pp. 927-930
    • Reid, J.1
  • 33
    • 65849488472 scopus 로고    scopus 로고
    • Intra-platform repeatability and inter-platform comparability of microRNA microarray technology
    • Sato,F. et al. (2009) Intra-platform repeatability and inter-platform comparability of microRNA microarray technology. PLoS One, 4, e5540.
    • (2009) PLoS One , vol.4 , pp. e5540
    • Sato, F.1
  • 34
    • 42649134796 scopus 로고    scopus 로고
    • Merging two gene-expression studies via cross-platform normalization
    • Shabalin,A. et al. (2008) Merging two gene-expression studies via cross-platform normalization. Bioinformatics, 24, 1154-1160.
    • (2008) Bioinformatics , vol.24 , pp. 1154-1160
    • Shabalin, A.1
  • 36
    • 60849119837 scopus 로고    scopus 로고
    • CMA: A comprehensive Bioconductor package for supervised classification with high dimensional data
    • Slawski,M. et al. (2008) CMA: A comprehensive Bioconductor package for supervised classification with high dimensional data. BMC Bioinformatics, 9, 439.
    • (2008) BMC Bioinformatics , vol.9 , pp. 439
    • Slawski, M.1
  • 37
    • 41349115501 scopus 로고    scopus 로고
    • Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation
    • Smith,D. et al. (2008) Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation. BMC Bioinformatics, 28, 63.
    • (2008) BMC Bioinformatics , vol.28 , pp. 63
    • Smith, D.1
  • 38
    • 77957935139 scopus 로고    scopus 로고
    • Genomic index of sensitivity to endocrine therapy for breast cancer
    • Symmans,W. et al. (2010) Genomic index of sensitivity to endocrine therapy for breast cancer. J. Clin. Oncol., 28, 4111-4119.
    • (2010) J. Clin. Oncol. , vol.28 , pp. 4111-4119
    • Symmans, W.1
  • 39
    • 27544451127 scopus 로고    scopus 로고
    • Simple decision rules for classifying human cancers from gene expression profiles
    • Tan,A. et al. (2005) Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics, 21, 3896-3904.
    • (2005) Bioinformatics , vol.21 , pp. 3896-3904
    • Tan, A.1
  • 40
    • 66549106409 scopus 로고    scopus 로고
    • A statistical framework to infer functional gene associations from multiple biologically interrelated microarray experiments
    • Teng,S. et al. (2007) A statistical framework to infer functional gene associations from multiple biologically interrelated microarray experiments. J. Am. Stat. Assoc., 104, 465-473.
    • (2007) J. Am. Stat. Assoc. , vol.104 , pp. 465-473
    • Teng, S.1
  • 41
    • 77957773218 scopus 로고    scopus 로고
    • Identification of gene expression signature in estrogen receptor positive breast carcinoma
    • Thakkar,A. et al. (2010) Identification of gene expression signature in estrogen receptor positive breast carcinoma. Biomark. Cancer, 2, 1-15.
    • (2010) Biomark. Cancer , vol.2 , pp. 1-15
    • Thakkar, A.1
  • 42
    • 48949119363 scopus 로고    scopus 로고
    • Evaluation of biological pathways involved in chemotherapy response in breast cancer
    • Tordai,A. et al. (2008) Evaluation of biological pathways involved in chemotherapy response in breast cancer. Breast Cancer Res., 10, R37.
    • (2008) Breast Cancer Res. , vol.10 , pp. R37
    • Tordai, A.1
  • 43
    • 84861414639 scopus 로고    scopus 로고
    • Comprehensive literature review and statistical considerations for microarray meta-analysis
    • Tseng,G. et al. (2012) Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res., 40, 3785-3799.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 3785-3799
    • Tseng, G.1
  • 44
    • 7044240645 scopus 로고    scopus 로고
    • Mutation of GATA3 in human breast tumors
    • Usary,J. et al. (2004) Mutation of GATA3 in human breast tumors. Oncogene, 23, 7669-7678.
    • (2004) Oncogene , vol.23 , pp. 7669-7678
    • Usary, J.1
  • 45
    • 0037137519 scopus 로고    scopus 로고
    • A gene-expression signature as a predictor of survival in breast cancer
    • van de Vijver,M. et al. (2002) A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med., 347, 1999-2009.
    • (2002) N. Engl. J. Med. , vol.347 , pp. 1999-2009
    • Van De Vijver, M.1
  • 46
    • 84926295116 scopus 로고    scopus 로고
    • Tumor cell migration screen identifies SRPK1 as breast cancer metastasis determinant
    • van Roosmalen,W. et al. (2015) Tumor cell migration screen identifies SRPK1 as breast cancer metastasis determinant. J. Clin. Invest., 125, 1648-1664.
    • (2015) J. Clin. Invest. , vol.125 , pp. 1648-1664
    • Van Roosmalen, W.1
  • 47
    • 18244409687 scopus 로고    scopus 로고
    • Gene expression profiling predicts clinical outcome of breast cancer
    • van't Veer,L. et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature, 415, 530-536.
    • (2002) Nature , vol.415 , pp. 530-536
    • Van't Veer, L.1
  • 48
    • 84858990934 scopus 로고    scopus 로고
    • Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder
    • Wang,X. et al. (2012) Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder.BMC Bioinformatics, 13, 13-52.
    • (2012) BMC Bioinformatics , vol.13 , pp. 13-52
    • Wang, X.1
  • 49
    • 27544492493 scopus 로고    scopus 로고
    • Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data
    • Xu,L. et al. (2005) Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics, 20, 3905-3911.
    • (2005) Bioinformatics , vol.20 , pp. 3905-3911
    • Xu, L.1
  • 50
    • 41749099668 scopus 로고    scopus 로고
    • Merging microarray data from separate breast cancer studies provides a robust prognostic test
    • Xu,L. et al. (2008) Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC Bioinformatics, 9, 125.
    • (2008) BMC Bioinformatics , vol.9 , pp. 125
    • Xu, L.1
  • 51
    • 49149121975 scopus 로고    scopus 로고
    • PCDH8, the human homolog of PAPC, is a candidate tumor suppressor of breast cancer
    • Yu,J. et al. (2008) PCDH8, the human homolog of PAPC, is a candidate tumor suppressor of breast cancer. Oncogene., 27, 4657-4665.
    • (2008) Oncogene. , vol.27 , pp. 4657-4665
    • Yu, J.1
  • 52
    • 84866450351 scopus 로고    scopus 로고
    • Frequent silencing of protocadherin 8 by promoter methylation, a candidate tumor suppressor for human gastric cancer
    • Zhang,D. et al. (2012) Frequent silencing of protocadherin 8 by promoter methylation, a candidate tumor suppressor for human gastric cancer. Oncol. Rep., 28, 1785-1791.
    • (2012) Oncol. Rep. , vol.28 , pp. 1785-1791
    • Zhang, D.1
  • 53
    • 84881257906 scopus 로고    scopus 로고
    • Breast cancer index identifies early-stage estrogen receptor-positive breast cancer patients at risk for early-and late-distant recurrence
    • Zhang,Y. et al. (2013) Breast cancer index identifies early-stage estrogen receptor-positive breast cancer patients at risk for early-and late-distant recurrence. Clin. Cancer Res., 19, 4196-4205.
    • (2013) Clin. Cancer Res. , vol.19 , pp. 4196-4205
    • Zhang, Y.1


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